The hygiene hypothesis suggests that parasitic infection modulates host immune responses and decreases atopy, but other data suggest parasitic infections may induce allergic responsiveness as well. To investigate the impact of molecular similarity among allergens and cross-reactive homologous helminth proteins in IgE-based serologic assessment of allergic disorders in helminth-infected population, we used multiplexed assays in filarial-infected and non-infected individuals for IgE measurements to allergen extracts that contained proteins with high levels of homology with helminth proteins and IgE against representative recombinant allergens with and without helminth homologues were performed. The impact of helminth infection on the levels and function of the IgE to these specific homologous and non-homologous allergens was corroborated in an animal model. We found that having a tissue-invasive filarial infection increased the serological prevalence ofIgE directed against house dust mite and cockroach, but not against timothy grass, the latter with few allergens with homologues in helminth infection. IgE ELISA confirmed that filaria-infected individuals had higher IgE prevalences to those recombinant allergens that had homologues in helminths. Mice infected with helminth Heligmosomoides polygyrus displayed increased levels of IgE and positive skin tests to allergens with homologues in the parasite. These results show that cross-reactivity among allergens and helminth proteins can have practical implications altering serologic approaches to allergen testing and brings a new perspective to the Hygiene Hypothesis. We have extended these findings to the level of the T cell. Using cells from individuals with filarial infection (with or without allergic disease) and those from uninfected individuals (with or without allergic disease), we have shown that parasite antigen (and their aero-allergen orthologues) drives a CD4+ IL-4/IL-13 dominated response in filarial infection that is augmented when the subject is also allergic when measured using multiparameter flow cytometry or multiplexed cytokine measurements.